title: Human islets, Sample VII

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

data_processing:
The raw data was filtered with cutadapt (Martin, 2011) to remove adapter sequences, ambiquous (N) and low quality bases (Phred score < 25). We also excluded read pairs that were too short (<25bp) after trimming.
The filtered reads were mapped to the human reference genome (GRCh38) with STAR aligner (Dobin et al., 2013).
Gene expression was counted from read pairs mapping to exons using featureCount in Rsubreads (Liao, Smyth and Shi, 2019). Duplicates, chimeric and multimapping reads were excluded, as well as reads with low mapping score (MAPQ < 10).
The read count data was analyzed with DESeq2 (Love, Huber and Anders, 2014). We compared the islets for organ donors to stem cell-derived islets (differentiated to stage7).
Assembly: GENCODE-GRCh38.p13
Supplementary files format and content: comma-delimited text file (csv); DESeq2 results and raw read counts per sample

source_name: pancreatic islets

growth_protocol: Human embryonic cell line H1 was cultured on Matrigel-coated plates in E8 medium and passaged using EDTA. To prepare the differentiation experiments, near-confluent plates of stem cells were dissociated using EDTA and seeded on new Matrigel coated plates in E8 supplemented with 0.5-uM Rho-Associated kinase inhibitor to achieve confluent plates.

extract_protocol:
Total RNA was extracted using the RNeasy® Plus Micro Kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: ES cells were dissociated with 5 mM EDTA treatment for 10 min and seeded at 1.5-2 million cells/3.5 cm well on Matrigel-coated plates with E8 medium containing 5 μM ROCK inhibitor (Y-27632 2HCl, Selleckchem). Differentiation was started 24 h later and proceeded through 7 stages differentiation protocol (Stages 1 to 4 in adherent culture and stages 5 to 7 in suspension culture): - Definitive endoderm induction (3 days): cells were washed 1xPBS (without Ca2+/Mg2+) and 2 mL medium/3.5 cm well of differentiation media was applied: MCDB131 (10372-019, Life Technologies) + 2mM Glutmax (35050038, Life Technologies) + 1.5 g/L NaHCO3 (Sigma-Aldrich) + 0.5% BSA fraction V Fatty acid free (Sigma-Aldrich) + 10 mM final glucose (Sigma-Aldrich) + 100 ng/ml ActA + 3 μM CHIR. CHIR concentration was reduced to 0.3 μM and 0 μM on day 1 and day 2 respectively. - Stage 2 posterior foregut induction (for 3 days, medium changed every day): MCDB131 + 2mM Glutmax + 1.5 g/L NaHCO3 + 0.5% BSA fV + 10 mM final glucose + 0.25 mM Ascorbic acid (A4544, Sigma-Aldrich) + 50 ng/mL FGF7 (Z03047, Genscript) - Stage 3 pancreatic endoderm induction (for 2 days, medium changed every day): MCDB131 + 2mM Glutmax + 2.5 g/L NaHCO3 + 2% BSA fV + 10 mM final glucose + 0.25 mM Ascorbic acid + 50 ng/mL FGF7 + 0.25 μM SANT1 (S4572, Sigma-Aldrich) + 1 μM RA + 100 nM LDN + 1:200 ITS-X (51500-056, Life Technologies) + 200 nM TPB (sc-204424, Santa Cruz). - Stage 4 pancreatic progenitor induction (3 days, medium changed every day): MCDB131 + 2mM Glutmax + 2.5 g/L NaHCO3 + 2% BSA fV + 10 mM final glucose + 0.25 mM Ascorbic acid + 2 ng/mL FGF7 + 0.25 μM SANT1 + 0.1 μM RA + 200 nM LDN + 1:200 ITS-X + 100 ng/mL EGF (AF-100-15, Peprotech) + 10 mM Nicotinamide (N0636, Sigma-Aldrich). - Stage 5 endocrine induction: Cells were washed 2x with EDTA, treated with TrypLE for 10 min at 37ºC, 1 mL/3.5 cm well. Cells were dissociated by pipetting, and spin down for 3 min at 200 rcf. Cells were resuspended in S5 medium with ROCK inhibitor at 10 uM, at a density of one million cells/mL, in a volume of 5 mL, in ultra-low attachment 6-well plates (3471, Corning) and placed in a rotating platform (InforsHT, Celltron) at 95 rpm in the incubator. After 24h, cells formed round aggregates and medium was changed to S5 without ROCK inhibitor: S5 medium (for 4 days, changed every day): MCDB131 + 2mM Glutmax + 1.5 g/L NaHCO3 + 2% BSA fV + 20 mM final Glucose + 1:200 ITS-X + 10 ug/mL Heparin (H3149, Sigma-Aldrich) + 0.25 μM SANT1 + 0.05 μM RA + 100 nM LDN + 10 μM ALK5inhII (S7233, Selleckchem) + 1 μM GC1 (4554, Tocris) + 10 μM Zinc Sulfate (Z0251, Sigma-Aldrich) + 20 ng/mL Betacellulin (100-50, Peprotech) + 100 nM GSiXX (565789, Millipore). - Stage 6 media (14 days, change every second day): MCDB131 + 2mM Glutmax + 1.5 g/L NaHCO3 + 2% BSA fV + 20 mM final glucose + 1:200 ITS-X + 10 ug/mL Heparin + 100 nM LDN + 10 μM ALK5inhII + 1 μM GC1 + 100 nM GSiXX + 10 μM Zinc Sulfate. - Stage 7 media (7 days, change every second day): MCDB131 + 2mM Glutmax + 1.5 g/L NaHCO3 + 2% BSA fV + 20 mM final glucose + 1:200 ITS-X + 10 ug/mL Heparin + 10 μM ALK5inhII + 1 μM GC1 + 10 μM Trolox + 1 mM N-Acetylcysteine (A9165, Sigma-Aldrich) + 75 μM Resveratrol (R5010, Sigma-Aldrich) + 20 μM JNK inhibitor (SP600125, #1496, Tocris) + 2 μM R428 (S2841, Selleckchem).

value: pancreatic islets

value: islets from organ donors


title: ChIPseq of H3K27ac in W22 roots Rep2

status: Public on May 22 2024

type: SRA

city: Cold Spring Harbor

first: Jonathan

last: Cahn

state: NY

address: 1 Bungtown Rd

country: USA

institute: CSHL

library_source: genomic

data_processing:
Adapter trimming with cutadapt
Mapping to each respective genome with bowtie2 (parameters:  --end-to-end --maxins 1500)
For Input, coverage tracks (bigwig) were created with deeptools bamCoverage
For IP, peaks were identified by calling peak with macs2 using the corresponding Input control. H3K4me1 broad peaks were called with parameter --broad, the other IPs narrow peaks were called with --call-summits.
For TF IP, tracks of log fold change enrichment of IP over Input were created with deeptools bamCompare (parameters: --scaleFactorsMethod "None" --normalizeUsing CPM --extendReads 300)
Assembly: B73 NAM; NC350 NAM; W22 v2; TIL11 v1.1
Supplementary files format and content: For Input: bigiwig file (coverage) for histone, logFC IP/Input for TFs.
Supplementary files format and content: For IP: list of identified peaks (macs2 narrowPeak or broadPeak format)

molecule: genomic DNA

organism: Zea mays

source_name: root tips

growth_protocol: For collecting immature ears, maize inbreds were grown in the CSHL Uplands Farm field in the summer until they reached the appropriate stage. The plants were collected from the field, and 5-10mm primary and secondary ear primordia were dissected in the lab then frozen in LN2 and stored at -80°C. TIL11 plants were grown in CSHL Upland Farm field from September to early October to promote floral transition by natural short day conditions. Immature TIL11 ears at an equivalent development stage (with inflorescence meristems, spikelet pair meristems, spikelet meristems and floral meristems) were collected under a dissecting microscope, frozen in LN2 stored at -80°C. For endosperm samples, ears of field-grown plants were sib-pollinated and collected 15 DAP. Endosperm was dissected in the lab, frozen in LN2 and stored in -80°C. For root tips samples, seeds were germinated on wet paper towels in a Pyrex dish kept in the incubator at 26°C in continuous darkness. After 5 days, 1-3 mm root tips were cut off with a razor blade on ice, frozen in LN2 and stored at -80°C. For coleoptilar nodes samples, seeds were germinated in flats in a long day (8h dark/16h light) growth chamber, 27°C day and 24°C night, and light at 130 μmoles at the top flat. After 5 days, seedlings were unearthed and 5 mm sections around coleoptilar nodes were dissected on ice, frozen in LN2 and stored at -80°C. For TFs ChIPseq, TU1A-YFP (Han, Jackson, and Martienssen 2012), and GT1-YFP (Whipple et al. 2011) transgenic lines were introgressed into the bd1;Tunicate (bd1;Tu) double mutant background, which produces highly proliferative ears, to generate large amounts of ear tissue.

extract_protocol:
For histone ChIPseq, chromatin was extracted as previously described (Villar and Köhler 2010). Briefly, tissue was crosslinked with 1% formaldehyde, ground and sheared with Covaris ultrasonicator. Mixture of Dynabeads with proteins A and G (1:1) (Invitrogen) was used for the IP and DNA was purified using ChIP Clean-up and Concentrator kit (Zymo Research). For TFs ChIP-seq, chromatin was extracted as previously described (Xu et al. 2021).
Histone ChIPseq libraries were constructed using Ultra II DNA kit (NEB). TF ChIP-seq libraries were constructed with NEXTflex ChIPseq kit (PerkinElmer Applied Genomics)

tag: tissue

value: root tips

tag: inbred line

tag: genotype

value: WT

tag: antibody

value: H3K27ac (Abcam, ab4729)


title: Human islets, Sample VI

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: a375_pool_run2_multiplex_CMO_C_to_T4,sequencing run 2,scRNA-Seq

city: New York

first: Itai

last: Yanai

address: 435 East. 30th St.

institute: NYU Langone Health

description: expression counts for all samples including untreated (C) and adapted cells from 30 nM to 4 uM of dabrafenib. Sample ids are attached to cell barcode names (column names).

library_source: transcriptomic single cell

data_processing:
Raw reads were processed with the CellRanger v7.0.0 (10X genomics) pipeline using cellranger count command with default parameters and with the hg38/GRCh38 genome and Ensembl 93 transcriptome references. Sample demultiplexing was performed with the CellRanger v7.0.0 (--min-assignment-confidence 0.8) and the Fastq files and CMO IDs indicated in the config file according to the cell ranger 7.0 manual. For the A375 experiment, the correspondence between samples and CMO tags are: C: CMO301; T003: CMO302; T006: CMO303; T0125: CMO304; T0250: CMO305; T0500: CMO306; T1: CMO307; T2: CMO308 and T4: CMO309). For the PC9 experiment, the correspondence between samples and CMO tags are: C: CMO301; T0008: CMO302; T0016: CMO303; T0032: CMO304; T0075: CMO305; T0150: CMO306; T0300: CMO307; T0600: CMO308; T1.2: CMO309; P1.2: CMO310
Assembly: hg38/GRCh38
Supplementary files format and content: a375_all_C_to_T4.csv.gz, count expression matrix for A375 cells. Sample ids are attached to cell barcode names (column names). Cells were filtered based on expression of less than 20% of mitochondrial genes, more than 500 genes, more than 700 umis expressed and less than average plus two standard deviations of umi counts. Rows are protein coding genes expressed in at least 1% of the cells.
Supplementary files format and content: pc9_all_C_to_T1.2_P1.2.csv.gz, count expression matrix for PC9 cells. Sample ids are attached to cell barcode names (column names). Cells were filtered based on expression of less than 20% of mitochondrial genes, more than 500 genes and more than 700 umis expressed and less than average plus two standard deviations of umi counts. Rows are protein coding genes expressed in at least 1% of the cells.

source_name: Cell line

growth_protocol: PC9 cells were cultured in RPMI-1640 (ThermoFisher) with 10% Fetal Bovine Serum (FBS), 1% L-Glutamine 200 mM, 1% Penicillin and Streptomycin (10,000 U/mL, ThermoFisher). A375 cells were cultured in DMEM (ThermoFisher) supplemented with 10% FBS, 1% L-Glutamine and 1% Penicillin and Streptomycin.

extract_protocol:
Cells were trypsinized and single-cell suspensions were counted and pooled for cell tagging method using the 10X Genomics CellPlex kit Set A according to manufacturers protocol. The cell pool was loaded for droplet-based scRNA-Seq using the 10X Genomics Chromium platform according to the manufacturer's protocol.
Library preparation was performed using the 10X Genomics Chromium platform with the Chromium Single Cell Library & Gel Bead Kit v3.1 following the manufacturer’s instructions. For sample pooling, cell suspensions from each corresponding sample were labeled using the 10X Genomics 3’ CellPlex kit Set A according to the manufacturer’s instructions. Cells were pooled in equal amounts and loaded in the 10X Genomics Chromium Controller. For A375 experiment, the correspondence between samples and CMO tags are: C: CMO301; T003: CMO302; T006: CMO303; T0125: CMO304; T0250: CMO305; T0500: CMO306; T1: CMO307; T2: CMO308 and T4: CMO309). For the PC9 experiment, the correspondence between samples and CMO tags are: C: CMO301; T0008: CMO302; T0016: CMO303; T0032: CMO304; T0075: CMO305; T0150: CMO306; T0300: CMO307; T0600: CMO308; T1.2: CMO309; P1.2: CMO310

treatment_protocol: A375 cells were treated in dose escalation from 30 nM to 4 uM of dabrafenib, generating populations resistant to 30 nM, 60 nM, 125 nM, 250 nM, 500 nM, 1 uM, 2 uM and 4 uM (T003, T006, T0125, T0250, T0500, T1, T2 and T4) plus untreated control (C). PC9 cells were treated in dose escalation from 8nM to 1.2 uM of osimertinib, generating resistant populations to 8 nM, 16 nM, 32 nM, 75 nM, 150 nM, 300 nM, 600 nM and 1.2 uM  (T0008, T0016, T0032, T0075, T0150, T0300, T0600, T1.2) plus untreated control (C). A population of persister cells was generated by acute exposure to 1.2 uM (P1.2)

value: Cell line

tag: cell line

value: melanoma

value: untreated and resistant cells from 30 nM to 4 uM of dabrafenib


title: Human islets, Sample IV


title: Input for ChIPseq in W22 endosperm Rep2

source_name: endosperm

value: endosperm


title: a375_pool_run1_C_to_T4,sequencing run 1,scRNA-Seq


title: Input for ChIPseq in W22 endosperm Rep1


title: scRNAseq_CITEseq_CD34+cells_2DGaK_HTO

city: Paris

first: Laëtitia

last: RACINE

address: 27 rue de Chaligny

country: France

institute: EPHE

data_processing:
Demultiplexing + Matrix generation with Cellranger (pipeline version cellranger-6.0.1)
R (version 4.2.1) & Seurat (version 4.3.0) & sctransform (version 0.3.5) & ggplot2 (version 3.4.2) & org.Hs.eg.db (version 3.15.0) & clusterProfiler (version 4.4.4) & ReactomeGSA (v1.10.0) & ReactomeContentService4R (v1.2.0)
Filters : 1000<number of genes detected in a cell<6500, <25%mRNA, >5%rRNA, mitochondrial genes removed, genes detected in more than 3 cells
Assembly: hg38 (GRCh38)
Supplementary files format and content: cell ranger outputs

molecule: polyA RNA

source_name: Umbilical cord blood

growth_protocol: CD34+ cells were purified from human healthy cord blood with a two-step immunomagnetic beads protocol and were then frozen in a cryopreservation medium. After thawing, CD34+ cells were cultured in a 96-well plate in a humidified 5% CO2 incubator at 37°C. Cells were grown in prestimulation medium made of X-Vivo (Lonza) supplemented with penicillin/streptomycin (respectively 100U/mL and 100µg/mL - Gibco, Thermo Scientific), 50 ng/ml h-FLT3, 25 ng/ml h-SCF, 25 ng/ml h-TPO, 10 ng/ml h-IL3 (Miltenyi) final concentration.

extract_protocol:
High viability percentage was obtained using a Dead Cell Removal kit (Miltenyi). scRNA-seq with feature barcoding technology for cell surface protein was performed as described in the Chromium Next GEM Single Cell 3’ protocol for v3.1 from 10X Genomics (CG000206 Rev D). 20 000 cells were loaded on the chip to obtain around 5000 cells encapsidated in GEM.
Library was prepared following the 10X Genomics protocol and sequenced on a NextSeq 500/550.
scRNA-seq combined with CITE-seq

treatment_protocol: Cells were stimulated with cytokines after thawing and were grown in the same medium with or without metabolic inhibitor (2-DG, DON or AOA) until lysis was performed. Cells were collected and lysed after 96h of cytokine stimulation.

value: Umbilical cord blood

tag: disease state

value: Healthy

value: CD34+ cells

value: 2DG 1mM + aK 5mM

tag: library type

value: HTO

tag: hto

value: TotalSeq A0251 anti-human hashtag1, TotalSeq A0252 anti-human hashtag2


title: ChIPseq of H3K4me3 in W22 endosperm Rep1

value: H3K4me3 (Millipore, 07-473)


title: Human islets, Sample I


title: pc9_pool_multiplex_CMO_C_to_T1.2_P1.2,scRNA-Seq

description: expression counts for all samples including untreated (C) and adapted cells from 8 nM to 1.2 uM of osimertinib plus persister cells treated with 1.2 uM of osimertinib. Sample ids are attached to cell barcode names (column names).

value: Epithelial, lung adenocarcinoma

value: EGFR-del

value: untreated and resistant cells from 8 nM to 1.2 uM of osimertinib plus persister cells treated with 1.2 uM of osimertinib for 9 days (P1.2)


title: RB1_NC

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

country: China

institute: Institute of Urological Cancer, Central South University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: prostate

growth_protocol: 22RV1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: prostate

value: 22RV1 cells

value: prostate cancer cells

value: the control group of knockdown of RB1 by siRNA

value: transfection infection


title: scRNAseq_CITEseq_CD34+cells_2DGaK_ADT

value: ADT

tag: adt

value: TotalSeq A0126 anti-human CD133, TotalSeq A0054 anti-human CD34


title: ChIPseq of H3K4me1 in W22 endosperm Rep1

value: endosperm

value: WT

value: H3K4me1 (Abcam, ab8895)


title: Stem cell-derived islets, Sample E

value: pancreatic islets

value: stem cell-derived islets

value: differentiation to stage 7 pancreatic islets


title: scRNAseq_CITEseq_CD34+cells_2DGaK_GEX

value: Umbilical cord blood

value: Healthy

value: CD34+ cells

value: 2DG 1mM + aK 5mM

value: mRNA


title: ChIPseq of H3K4me1 in W22 endosperm Rep2


title: Stem cell-derived islets, Sample D


title: ChIPseq of H3K27ac in W22 endosperm Rep2

value: H3K27ac (Abcam, ab4729)


title: scRNAseq_CITEseq_CD34+cells_AOAaK_ADT

value: AOA 1.9mM + aK 5mM


title: a375_pool_run1_multiplex_CMO_C_to_T4,sequencing run 1,scRNA-Seq

value: Cell line

value: melanoma

value: untreated and resistant cells from 30 nM to 4 uM of dabrafenib


title: scRNAseq_CITEseq_CD34+cells_AOAaK_GEX


title: ChIPseq of H3K27ac in W22 endosperm Rep1


title: Human islets, Sample V

value: islets from organ donors


title: Stem cell-derived islets, Sample B


title: Stem cell-derived islets, Sample C


title: ChIPseq of H3K27ac in W22 roots Rep1

value: root tips


title: Input for ChIPseq in W22 ears Rep2

source_name: immature ears

value: immature ears

value: WT


title: scRNAseq_CITEseq_CD34+cells_AOA_ADT

value: AOA 1.9mM

value: ADT

value: TotalSeq A0126 anti-human CD133, TotalSeq A0054 anti-human CD34


title: scRNAseq_CITEseq_CD34+cells_AOA_GEX

value: Umbilical cord blood


title: ChIPseq of H3K4me3 in W22 endosperm Rep2

value: endosperm

value: H3K4me3 (Millipore, 07-473)


title: Stem cell-derived islets, Sample A

value: pancreatic islets

value: stem cell-derived islets

value: differentiation to stage 7 pancreatic islets


title: Human islets, Sample II


title: a357_pool_run2_C_to_T4,sequencing run 2,scRNA-Seq


title: Human islets, Sample III


title: scRNAseq_CITEseq_CD34+cells_DONaK_CTRLaK_HTO

value: Healthy

value: CD34+ cells

value: Mixed samples (DON 2.5uM + aK 5mM, Untreated + aK 5mM)

value: HTO

value: TotalSeq A0251 anti-human hashtag1, TotalSeq A0252 anti-human hashtag2


title: Input for ChIPseq in W22 ears Rep1


title: Human_PFC_Hi-C

city: Beijing

first: Ying

last: Liu

address: 5 Summer Palace Road, Haidian District, Beijing

department: College of Future Technology

institute: Peking University

description: Hi-C of PFC of adult human

data_processing:
Basecalling was performed using Illunima Casava (version: 1.8).
We used HiC-Pro (version: 2.11.1) to perform preprocessing for Hi-C data of PFC of human and rhesus macaque. Paired-end reads in FASTQ file format were first aligned against the reference genome (GRCh38/hg38 for human and rheMac10Plus (40 gaps filling based on Mmul_10/rheMac10)  for rhesus macaque) using Bowtie 2 (version: 2.3.5) with following parameters, global mapping: -very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder; local mapping: -very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder.
Stringent filtering processes were performed following HiC-Pro standard workflow to generate genome-wide valid contact pairs.
Cooltools (version: 0.8.8) was used to identify A/B compartments at 100 Kb resolution, with the genome divided into two distinct groups based on the sign of the first PC (PC1). The group with higher gene density was defined as compartment A, and the other was compartment B. TAD boundaries were detected using the insulation score method (Crane et al., 2015) at a resolution of 40 Kb. Consequently, TAD bodies were defined as genomic regions between two adjacent boundaries. Chromatin loops were called by HiCCUPS (version: 1.9.9) at 25 Kb resolution.
Assembly: Mmul_10 (40 gaps filling)
Supplementary files format and content: *.bed files refer to the genomic coordinates of 3D genome organizations, including A/B compartments, TADs and TAD boundaries.
Supplementary files format and content: *bedpe files refer to the genomic coordinates of chromatin loops.

source_name: Brain

extract_protocol:
0.2 g frozen PFC sample was ground in liquid nitrogen and prepared into cell suspension. The filtered cell suspensions were fixed in 1% formaldehyde for 30 min. The cross-linked DNA was digested with 200U MboI, and the digested fragment ends were filled with biotin-14-dATP, dCTP, dGTP and dTTP by DNA Polymerase I Klenow Fragment (NEB, #M0210L). The resulting blunt-end fragments were re-ligated by T4 DNA ligase. Then, the ligated cross-linked DNA was reversed by proteinase K. DNA purification was performed by removing biotin from unligated ends using T4 DNA polymerase. The resulting purified DNA was sheared to a length of 350~500 bp using Covaris M220 and biotin-labeled DNA was pulled down with Dynabeads M-280 Streptavidin (Invitrogen). The library preparation including end repair, adapter ligation and PCR amplification was performed using DNA library preparation kit (Vazyme, #ND607). The resulting libraries were sequenced by Illumina 150 bp paired-end sequencing.
Hi-C libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina® V3 (Vazyme, #ND607) following manufacturer's instructions.

value: Wild type

tag: Sex

value: Male

tag: age

value: 45 years old

value: Prefrontal cortex (PFC)


title: ChIPseq of H3K4me3 in W22 ears Rep2

value: immature ears

value: WT


title: scRNAseq_CITEseq_CD34+cells_DONaK_CTRLaK_ADT

value: Umbilical cord blood

value: ADT

value: TotalSeq A0126 anti-human CD133, TotalSeq A0054 anti-human CD34


title: 053T

city: Guangzhou

first: jinhuan

last: wei

address: No.58 zhongshan 2rd Road

institute: SYSU

data_processing:
RNA-Seq paired-end clean data obtained were then analyzed using Hisat2, Samtools-1.9, Stringtie 1.3.5 and DESeq2.
Human reference genome (Homo_sapiens.GRCh38.84.gtf.gz) was obtained from Ensembl (ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.gtf.gz).
The genes annotated by GENCODE version 22 were used.
Genome_build: Homo_sapiens.GRCh38.84.gtf
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Renal papillary cell carcinoma

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tumor

value: Normal renal tissue


title: ChIPseq of H3K4me3 in W22 ears Rep1

value: H3K4me3 (Millipore, 07-473)


title: scRNAseq_CITEseq_CD34+cells_DONaK_CTRLaK_GEX

value: Healthy

value: mRNA


title: 053N

value: Normal

value: Tumor tissue


title: scRNAseq_CITEseq_CD34+cells_DON_2DG_HTO

value: CD34+ cells

value: Mixed samples (2DG 1mM, DON 2.5uM)

value: HTO

value: TotalSeq A0251 anti-human hashtag1, TotalSeq A0252 anti-human hashtag2


title: 052T


title: ChIPseq of H3K4me1 in W22 ears Rep2

value: H3K4me1 (Abcam, ab8895)


title: ChIPseq of H3K4me1 in W22 ears Rep1

value: immature ears


title: 052N


title: scRNAseq_CITEseq_CD34+cells_DON_2DG_GEX


title: ChIPseq of H3K27ac in W22 ears Rep1

value: WT

value: H3K27ac (Abcam, ab4729)


title: ChIPseq of H3K27ac in W22 ears Rep2


title: Input for ChIPseq in W22 coleoptilar nodes Rep2

source_name: coleoptilar nodes

value: coleoptilar nodes


title: 051N


title: scRNAseq_CITEseq_CD34+cells_CTRL2_ADT

value: Umbilical cord blood

value: Untreated

value: ADT

value: TotalSeq A0126 anti-human CD133, TotalSeq A0054 anti-human CD34


title: scRNAseq_CITEseq_CD34+cells_DON_2DG_ADT

value: Healthy


title: scRNAseq_CITEseq_CD34+cells_CTRL2_GEX

value: mRNA


title: 050T

value: Tumor

value: Normal renal tissue


title: Input for ChIPseq in W22 coleoptilar nodes Rep1


title: scRNAseq_CITEseq_CD34+cells_CTRL1_ADT

value: CD34+ cells


title: ChIPseq of H3K4me3 in W22 coleoptilar nodes Rep2

value: H3K4me3 (Millipore, 07-473)


title: scRNAseq_CITEseq_CD34+cells_CTRL1_HTO

value: HTO

value: TotalSeq A0251 anti-human hashtag1


title: 049T


title: ChIPseq of H3K4me3 in W22 coleoptilar nodes Rep1


title: scRNAseq_CITEseq_CD34+cells_CTRL1_GEX


title: 049N

value: Normal

value: Tumor tissue


title: bulkATACseq_CD34+_AOA_24h_rep3

description: bulk ATAC seq - Fast ATAC protocol

data_processing:
Cleaning and alignment of data using : trimmomatic (v0.32), bowtie2 (v2.4.1), samtools (v1.4), macs2 (v2.1.1), picard (v1.138) and bedtools (v.2.29.2)
Snakemake (v7.25.0) workflow to handle bam files : merge biological donors (samtools merge v1.11), index the files, quality control checking and count reads.
A downsampling step with samtools view function was performed as regard to the smallest number of reads detected in the cohort (80 000 000 reads)
A new peak calling was conducted on downsampled .bam files using the macs2 callpeak tool (v2.2.7.1) with the following parameters: <-f BAMPE -g hs -B –broad –broad-cutoff 0.1>.
R (v4.2.1) & Rsubread (v2.4.0) & GenomicRanges (v1.42.0) & DEseq2 (v1.38.3) & ggplot2 (v3.4.2)
Only peaks with 10 or more reads were kept for further analysis.
Assembly: hg19
Supplementary files format and content: xxx_threshold_10_ann.gr.rds files are genomic ranges object for R scripts. Biological replicates for the same condition and time point were merged and filter on the minimal number of reads per peak was applied.

extract_protocol:
Living cells were isolated before transposition by FACS using 7-AAD labeling. Around 5000 cells for each sample were used.
Library was prepared following the Fast ATAC-seq protocol, controled with Bioanalyzer and sequenced with NextSeq or MiSeq system.

treatment_protocol: Cells were stimulated with cytokines after thawing and were grown in the same medium with or without metabolic inhibitor (2-DG, DON or AOA) until lysis was performed. Cells were collected and lysed after 03h, 12h or 24h of cytokine stimulation.

value: AOA 1.9mM


title: ChIPseq of H3K4me1 in W22 coleoptilar nodes Rep2

value: WT

value: H3K4me1 (Abcam, ab8895)


title: ChIPseq of H3K4me1 in W22 coleoptilar nodes Rep1

value: coleoptilar nodes


title: bulkATACseq_CD34+_AOA_24h_rep2

description: bulk ATAC seq - Fast ATAC protocol

value: Umbilical cord blood


title: 048N


title: ChIPseq of H3K27ac in W22 coleoptilar nodes Rep2

value: H3K27ac (Abcam, ab4729)


title: 048T


title: 047T


title: 051T


title: ChIPseq of H3K27ac in W22 coleoptilar nodes Rep1


title: bulkATACseq_CD34+_AOA_12h_rep2

description: bulk ATAC seq - Fast ATAC protocol


title: Input for ChIPseq in TIL11 ears Rep2

value: immature ears


title: bulkATACseq_CD34+_AOA_12h_rep3

description: bulk ATAC seq - Fast ATAC protocol

value: Healthy


title: 047N


title: 046N


title: 050N


title: bulkATACseq_CD34+_AOA_12h_rep1

description: bulk ATAC seq - Fast ATAC protocol


title: ChIPseq of H3K27ac in TIL11 ears Rep2


title: 046T


title: bulkATACseq_CD34+_AOA_03h_rep3

description: bulk ATAC seq - Fast ATAC protocol


title: Input for ChIPseq in TIL11 ears Rep1


title: ChIPseq of H3K27ac in TIL11 ears Rep1


title: 045N


title: 045T


title: bulkATACseq_CD34+_AOA_03h_rep1

description: bulk ATAC seq - Fast ATAC protocol


title: 044T


title: bulkATACseq_CD34+_AOA_03h_rep2

description: bulk ATAC seq - Fast ATAC protocol


title: Input for ChIPseq in NC350 roots Rep2

value: root tips


title: ChIPseq of H3K4me3 in NC350 roots Rep2


title: 044N


title: Input for ChIPseq in NC350 roots Rep1


title: bulkATACseq_CD34+_DON_24h_rep2

description: bulk ATAC seq - Fast ATAC protocol

value: DON 2.5uM


title: 043T

value: Tumor

value: Normal renal tissue


title: bulkATACseq_CD34+_AOA_24h_rep1

description: bulk ATAC seq - Fast ATAC protocol

value: CD34+ cells


title: ChIPseq of H3K4me3 in NC350 roots Rep1

value: H3K4me3 (Millipore, 07-473)


title: bulkATACseq_CD34+_DON_24h_rep1

description: bulk ATAC seq - Fast ATAC protocol


title: 043N


title: ChIPseq of H3K4me1 in NC350 roots Rep2


title: bulkATACseq_CD34+_DON_12h_rep1

description: bulk ATAC seq - Fast ATAC protocol


title: ChIPseq of H3K4me1 in NC350 roots Rep1


title: 041T


title: bulkATACseq_CD34+_DON_12h_rep3

description: bulk ATAC seq - Fast ATAC protocol


title: 042T


title: Input for ChIPseq in NC350 endosperm Rep2

value: endosperm


title: bulkATACseq_CD34+_DON_03h_rep2

description: bulk ATAC seq - Fast ATAC protocol


title: bulkATACseq_CD34+_DON_03h_rep1

description: bulk ATAC seq - Fast ATAC protocol


title: 041N

value: Normal


title: 040N

value: Tumor tissue


title: 040T


title: Input for ChIPseq in NC350 endosperm Rep1


title: ChIPseq of H3K4me3 in NC350 endosperm Rep2


title: ChIPseq of H3K27ac in NC350 roots Rep1


title: bulkATACseq_CD34+_DON_03h_rep3

description: bulk ATAC seq - Fast ATAC protocol


title: bulkATACseq_CD34+_DON_12h_rep2

description: bulk ATAC seq - Fast ATAC protocol


title: ChIPseq of H3K4me3 in NC350 endosperm Rep1


title: bulkATACseq_CD34+_2DG_24h_rep2

description: bulk ATAC seq - Fast ATAC protocol

value: 2DG 1mM


title: 039N


title: 039T


title: ChIPseq of H3K4me1 in NC350 endosperm Rep2

value: WT


title: bulkATACseq_CD34+_2DG_24h_rep1

description: bulk ATAC seq - Fast ATAC protocol


title: bulkATACseq_CD34+_2DG_12h_rep3

description: bulk ATAC seq - Fast ATAC protocol


title: ChIPseq of H3K4me1 in NC350 endosperm Rep1

value: H3K4me1 (Abcam, ab8895)


title: 042N


title: 038T


title: 038N


title: bulkATACseq_CD34+_2DG_12h_rep2

description: bulk ATAC seq - Fast ATAC protocol


title: ChIPseq of H3K27ac in NC350 endosperm Rep2


title: 037T


title: ChIPseq of H3K27ac in NC350 endosperm Rep1


title: 037N


title: 036T


title: bulkATACseq_CD34+_2DG_03h_rep3

description: bulk ATAC seq - Fast ATAC protocol


title: Input for ChIPseq in NC350 ears Rep2


title: bulkATACseq_CD34+_2DG_03h_rep2

description: bulk ATAC seq - Fast ATAC protocol


title: 036N


title: Input for ChIPseq in NC350 ears Rep1


title: ChIPseq of H3K4me3 in NC350 ears Rep2


title: 035T


title: ChIPseq of H3K27ac in NC350 roots Rep2


title: 035N


title: bulkATACseq_CD34+_CTRL_24h_rep5

description: bulk ATAC seq - Fast ATAC protocol

value: Untreated


title: ChIPseq of H3K4me3 in NC350 ears Rep1


title: bulkATACseq_CD34+_CTRL_24h_rep4

description: bulk ATAC seq - Fast ATAC protocol

value: Umbilical cord blood


title: ChIPseq of H3K4me1 in NC350 ears Rep1


title: 034T


title: ChIPseq of H3K4me1 in NC350 ears Rep2


title: 034N


title: ChIPseq of H3K27ac in NC350 ears Rep2

value: H3K27ac (Abcam, ab4729)


title: 033T


title: ChIPseq of H3K27ac in NC350 ears Rep1

value: immature ears


title: bulkATACseq_CD34+_CTRL_24h_rep1

description: bulk ATAC seq - Fast ATAC protocol

value: Healthy


title: 033N


title: bulkATACseq_CD34+_CTRL_24h_rep3

description: bulk ATAC seq - Fast ATAC protocol


title: Input for ChIPseq in NC350 coleoptilar nodes Rep2

value: coleoptilar nodes


title: bulkATACseq_CD34+_2DG_03h_rep1

description: bulk ATAC seq - Fast ATAC protocol


title: bulkATACseq_CD34+_CTRL_12h_rep3

description: bulk ATAC seq - Fast ATAC protocol


title: Input for ChIPseq in NC350 coleoptilar nodes Rep1


title: bulkATACseq_CD34+_CTRL_12h_rep2

description: bulk ATAC seq - Fast ATAC protocol


title: 032N


title: 032T


title: ChIPseq of H3K4me3 in NC350 coleoptilar nodes Rep2


title: bulkATACseq_CD34+_CTRL_12h_rep1

description: bulk ATAC seq - Fast ATAC protocol


title: ChIPseq of H3K4me3 in NC350 coleoptilar nodes Rep1


title: bulkATACseq_CD34+_CTRL_03h_rep2

description: bulk ATAC seq - Fast ATAC protocol


title: 031T


title: 031N


title: bulkATACseq_CD34+_CTRL_03h_rep1

description: bulk ATAC seq - Fast ATAC protocol


title: 030T


title: bulkATACseq_CD34+_Xvivo_00h_rep2

description: bulk ATAC seq - Fast ATAC protocol

value: Untreated & no cytokins


title: 030N


title: ChIPseq of H3K4me1 in NC350 coleoptilar nodes Rep2


title: ChIPseq of H3K27ac in NC350 coleoptilar nodes Rep2


title: ChIPseq of H3K4me1 in NC350 coleoptilar nodes Rep1


title: bulkATACseq_CD34+_CTRL_24h_rep2

description: bulk ATAC seq - Fast ATAC protocol


title: bulkATACseq_CD34+_2DG_24h_rep3

description: bulk ATAC seq - Fast ATAC protocol


title: bulkATACseq_CD34+_Xvivo_00h_rep1

description: bulk ATAC seq - Fast ATAC protocol


title: ChIPseq of H3K27ac in NC350 coleoptilar nodes Rep1


title: 029N


title: 029T

value: Tumor


title: Input for ChIPseq in B73 roots Rep2

value: root tips


title: Kura_T320

data_processing:
Data processed according to Baron et al. (2020) The Stress-Like Cancer Cell State Is a Consistent Component of Tumorigenesis. Cell Syst. 18;11(5):536:546
https://github.com/flo-compbio/singlecell
Seurat 2.3.2
Assembly: hg38/GRCh38
Supplementary files format and content: csv

source_name: Kuramochi

growth_protocol: Cells were cultured in RPMI-1640 (ThermoFisher) with 10% Fetal Bovine Serum (FBS), 1% MEM Non-Essential Amino Acids, 1% L-Glutamine 200 mM, 1% Antibiotic-Antimycotic solution 100X and 0.25 U/mL insulin solution (Sigma-Aldrich)

extract_protocol: inDrop: Klein A. M., Mazutis L., Akartuna I., Tallapragada N., Veres A., et al. (2015) Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161: 1187-1201

treatment_protocol: Treated cells were exposed to olaparib concentrations as indicated until reaching confluency

value: Kuramochi

value: Epithelial

value: olaparib 320uM


title: 028T

value: Normal renal tissue


title: 028N

value: Normal

value: Tumor tissue


title: ChIPseq of H3K4me3 in B73 roots Rep2

value: WT

value: H3K4me3 (Millipore, 07-473)


title: bulkATACseq_CD34+_DON_24h_rep3

description: bulk ATAC seq - Fast ATAC protocol

value: CD34+ cells

value: DON 2.5uM


title: Kura_T40

value: olaparib 40uM


title: 027T


title: Kura_T20

value: olaparib 20uM


title: ChIPseq of H3K4me3 in B73 roots Rep1


title: 027N


title: 026T


title: ChIPseq of H3K4me1 in B73 roots Rep2

value: H3K4me1 (Abcam, ab8895)


title: 026N


title: ChIPseq of H3K4me1 in B73 roots Rep1


title: Kura_T5

value: olaparib 5uM


title: ChIPseq of H3K27ac in B73 roots Rep1

value: H3K27ac (Abcam, ab4729)


title: 025T

value: Tumor


title: Kura_T2.5

value: olaparib 2.5uM


title: ChIPseq of H3K27ac in B73 roots Rep2

value: root tips


title: Kura_T1

value: Kuramochi

value: Epithelial

value: olaparib 1uM


title: Kura_T160

value: olaparib 160uM


title: 025N

value: Normal

value: Tumor tissue


title: Input for ChIPseq in B73 endosperm Rep1

value: endosperm

value: WT


title: 024T

value: Normal renal tissue


title: Kura_T80

value: olaparib 80uM


title: IonXpress_023_R_2019_07_19_09_53_20_NGS50_libQ160_ML56d

city: Corbeil-Essonnes

first: MARGOT

last: JARRIGE

address: 28, Rue Henri Desbruères

institute: I-Stem/INSERM U861

data_processing:
Torrent_Suite 5,6,0
FASTQ file were generated with FastqCreator_jb v3.6.0-r57238 (799) on Torrent Suite
Fastq were import on Partek Flow software (v6 Partek Inc) and analyse using Partek Flow Pipeline for Ion Whole Transcriptome Analysis
differentially expressed genes between groups were quantified using Partek E/M algorithm normalised by the Total count/sample
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini or micro plus kit (Qiagen). 100ng of mRNA was used for the construction of sequencing libraries.
RNA libraries for 3'RNA-seq were prepared using Qunatseq mRNA Library Prep Kit following manufacturer's protocols.

value: hIPSC derived Medium Spiny neurons (MSN)

value: -/mut

value: CRISPR

tag: clone

tag: time


title: Input for ChIPseq in B73 endosperm Rep2


title: Input for ChIPseq in B73 roots Rep1


title: 024N


title: IonXpress_022_R_2019_02_26_15_45_33_NGS50_libQ159_ML56


title: Kura_T10

value: olaparib 10uM


title: 023T

value: Tumor


title: IonXpress_021_R_2019_02_26_15_45_33_NGS50_libQ158_ML61b


title: IonXpress_020_R_2019_02_26_15_45_33_NGS50_libQ157_ML54d


title: ChIPseq of H3K4me3 in B73 endosperm Rep2

value: H3K4me3 (Millipore, 07-473)


title: 023N


title: ChIPseq of H3K4me1 in B73 endosperm Rep1

value: H3K4me1 (Abcam, ab8895)


title: IonXpress_019_R_2019_07_19_09_53_20_NGS50_libQ156_ML62b


title: ChIPseq of H3K27ac in B73 endosperm Rep1

value: H3K27ac (Abcam, ab4729)


title: Kura_C

value: Kuramochi

value: Epithelial

value: Untreated


title: ChIPseq of H3K27ac in B73 endosperm Rep2


title: IonXpress_018_R_2019_02_26_15_45_33_NGS50_libQ155_ML55


title: 022N

value: Normal


title: 021N

value: Tumor tissue


title: 021T


title: Input for ChIPseq in B73 ears Rep1 H3K27ac/H3K4me1

value: immature ears


title: IonXpress_016_R_2019_02_26_15_45_33_NGS50_libQ153_ML53c


title: Input for ChIPseq in B73 ears Rep2 H3K27ac/H3K4me1

value: WT


title: IonXpress_015_R_2019_07_19_09_53_20_NGS50_libQ152_ML59c

value: wt/-


title: 020T

value: Normal renal tissue


title: Input for ChIPseq in B73 ears Rep2 H3K4me3


title: IonXpress_014_R_2019_02_26_15_45_33_NGS50_libQ151_ML52

value: hIPSC derived Medium Spiny neurons (MSN)


title: 020N


title: 019T


title: ChIPseq of H3K4me3 in B73 endosperm Rep1

value: endosperm


title: Input for ChIPseq in B73 ears Rep1 H3K4me3


title: 022T


title: ChIPseq of H3K4me1 in B73 endosperm Rep2


title: IonXpress_013_R_2019_02_26_15_45_33_NGS50_libQ150_ML57d

value: CRISPR


title: ChIPseq of H3K4me3 in B73 ears Rep2


title: 019N


title: IonXpress_012_R_2019_02_26_15_45_33_NGS50_libQ149_ML50d


title: IonXpress_017_R_2019_02_26_15_45_33_NGS50_libQ154_ML60b


title: ChIPseq of H3K4me3 in B73 ears Rep1


title: IonXpress_011_R_2019_07_19_09_53_20_NGS50_libQ148_ML58b

value: wt/mut

value: TAP


title: IonXpress_010_R_2019_02_26_15_45_33_NGS50_libQ147_ML58a


title: ChIPseq of H3K4me1 in B73 ears Rep2


title: IonXpress_009_R_2019_02_26_15_45_33_NGS50_libQ146_ML51d


title: ChIPseq of H3K4me1 in B73 ears Rep1


title: 017N


title: 018T

value: Tumor


title: IonXpress_008_R_2019_02_26_15_45_33_NGS50_libQ145_ML51b


title: 017T


title: 016T


title: IonXpress_047_R_2019_10_10_17_02_28_NGS56_libQ209

value: hiPSC

value: -/mut

value: Day 0


title: ChIPseq of H3K27ac in B73 ears Rep1

value: H3K27ac (Abcam, ab4729)


title: IonXpress_048_R_2019_10_10_17_02_28_NGS56_libQ210


title: 016N


title: ChIPseq of H3K27ac in B73 ears Rep2


title: Input for ChIPseq in B73 coleoptilar nodes Rep2

value: coleoptilar nodes


title: Input for ChIPseq in B73 coleoptilar nodes Rep1


title: 015N

value: Normal


title: 015T


title: ChIPseq of H3K4me3 in B73 coleoptilar nodes Rep2

value: H3K4me3 (Millipore, 07-473)


title: IonXpress_024_R_2019_10_11_14_46_22_NGS55_libQ208


title: IonXpress_023_R_2019_10_11_14_46_22_NGS55_libQ207


title: 014T


title: IonXpress_022_R_2019_10_10_17_02_28_NGS56_libQ206


title: 018N

value: Tumor tissue


title: IonXpress_021_R_2019_10_10_17_02_28_NGS56_libQ205


title: 013T


title: ChIPseq of H3K4me1 in B73 coleoptilar nodes Rep2

value: WT

value: H3K4me1 (Abcam, ab8895)


title: 013N


title: ChIPseq of H3K27ac in B73 coleoptilar nodes Rep1


title: 011T

value: Normal renal tissue


title: Feather-tailed possum (Sample1790)

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Short-read assembly using w2rap (Clavijo, 2017); Hi-C-guided genome assembly (Juicer, 3D-DNA, JBAT); RagTag assembler (Alonge et al., 2022) for Dactylopsila trivirgata and Distoechurus pennatus
Assembly: Generated as part of the study
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly; RagTag assisted assemblies for Dactylopsila trivirgata and Distoechurus pennatus
Library strategy: In situ Hi-C; ClaSeek PCR-free DNA-Seq.

organism: Distoechurus pennatus

source_name: liver

extract_protocol:
Extractions for WGS libraries were done using DNeasy blood & tissue kit
The Hi-C libraries were prepared following the in situ Hi-C strategy (Rao, Huntley et al., 2014). Briefly, cells or tissue were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. Afterward DNA was handled according to standard Illumina library construction protocol. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on various Illumina instruments following the manufacturer's protocols. Fpr the tammar wallaby, a short insert-size PCR-free DNA-Seq library was prepared following the ClaSeek protocol.

value: liver


title: ChIPseq of H3K4me1 in B73 coleoptilar nodes Rep1


title: IonXpress_014_R_2019_10_10_17_02_28_NGS56_libQ198


title: ChIPseq of H3K27ac in B73 coleoptilar nodes Rep2


title: IonXpress_020_R_2019_10_11_14_46_22_NGS55_libQ204


title: IonXpress_019_R_2019_10_11_14_46_22_NGS55_libQ203


title: 012T


title: 012N


title: 010N


title: 011N


title: IonXpress_016_R_2019_10_11_14_46_22_NGS55_libQ200

value: wt/-


title: Ground cuscus (Sample0438)

organism: Phalanger gymnotis

source_name: blood

value: blood


title: 010T


title: Western grey kangaroo (Sample1290)

organism: Macropus fuliginosus


title: IonXpress_017_R_2019_10_10_17_02_28_NGS56_libQ201

value: CRISPR


title: Hi-C of Elephas maximus indicus DNA Zoo Sample0030, Ultima sequencing

description:
HIC1381u_ASM1433276v1_HiC.hic
HIC1381u_ASM1433276v1_HiC_30.hic

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Reference-guided 3D genome assembly (Anonamos, 3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (BWA, Juicer, 3D-DNA)
liftover (KentUtils, 3D-DNA)
Gene annotation (TOGA)
Compartment annotation (CRUSH)
Loop calling and aggregate analysis (HiCCUPS, Juicer Tools, SIP, SIP META)
Aggregate chromosome analysis (3D-DNA)
Modeling of 3D structures of woolly mammoth chromosomes (OpenMiChroM)
DNA degradation simulations (NuChroM, custom script)
Assembly: The following existing genome builds were used in parts of the study: Loxafr3.0 (GCA_000001905.1), ASM1433276v1 (GCA_014332765.1), EquCab2.0 (GCF_000002305.2), ASM303372v1 (GCA_003033725.1), bosTau9 (GCF_002263795.3), ASM651725v1 (GCF_006517255.1), ASM3043605v1 (GCF_030436055.1), ASM331443v2 (GCF_003314435.2), hg38, hg19.
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences. In addition to "standard" hic maps build against chromosome-length references included are "assembly" maps generated by 3D-DNA for before and after genome assembly and an aggregate chromosome analysis (ACA) map.
Supplementary files format and content: bedpe: chromatin loops
Supplementary files format and content: bedgraph: A/B compartment annotations
Supplementary files format and content: sw: HDF5-based file for storing 3D structure ensembles
Supplementary files format and content: assembly: text file describing the relationship between the draft assembly and the chromosome-length upgrade
Supplementary files format and content: bed: gene annotations

organism: Elephas maximus indicus

source_name: blood: Ear vein

extract_protocol:
The protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Briefly, PaleoHi-C is a a modified in situ Hi-C protocol, tailored towards working with highly degraded samples. The principal modifications were: (i) immediate preservation in the field using ethanol to reduce microbial activity; and (ii) sequestration of chromatin bodies on beads; (iii) removal of shearing and size selection given the lack of high molecular weight DNA; and (iv) library amplification using a paleo-compatible workflow
Library contruction protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024.
Modified Hi-C.

value: blood:Ear vein


title: IonXpress_013_R_2019_10_10_17_02_28_NGS56_libQ197

value: wt/mut


title: IonXpress_012_R_2019_10_11_14_46_22_NGS55_libQ196

value: hiPSC


title: ChIPseq of H3K4me3 in B73 coleoptilar nodes Rep1


title: IonXpress_011_R_2019_10_11_14_46_22_NGS55_libQ195


title: Hi-C of Elephas maximus indicus DNA Zoo Sample0045, Ultima sequencing

description:
HIC1382u_ASM1433276v1_HiC.hic
HIC1382u_ASM1433276v1_HiC_30.hic


title: 014N


title: 009T

value: Tumor


title: 009N


title: IonXpress_018_R_2019_10_10_17_02_28_NGS56_libQ202

value: Day 0


title: Striped possum (Sample1783)

description: RagTag

organism: Dactylopsila trivirgata

source_name: kidney

value: kidney


title: Hi-C of Elephas maximus DNA Zoo Sample0045, part2

description:
ASM1433276v1.hic
ASM1433276v1_HiC.fasta.gz
ASM1433276v1.rawchrom.hic
EM_pbmc_Loxafr3.0_HiC.hic
EM_pbmc_Loxafr3.0_HiC_30.hic
EM_pbmc_MamPri_Loxafr3.0_assisted_HiC.hic
EM_pbmc_MamPri_Loxafr3.0_assisted_HiC_30.hic
EM_pbmc_MamPri_ASM1433276v1_assisted_HiC.hic
EM_pbmc_MamPri_ASM1433276v1_assisted_HiC_30.hic
HIC1382_ASM1433276v1_HiC.hic
HIC1382_ASM1433276v1_HiC_30.hic


title: Lung endothelial cells_Young_SARS-CoV-2 infected, biological replicate 4

city: Boston

first: Markus

last: Bosmann

state: MA

address: 72 E Concord Street

department: Pulmonary Centre, Department of Medicine

institute: Boston University

data_processing:
The genome and gtf of Mus musculus (Gencode version M27; GRCm39) and Severe acute respiratory syndrome coronavirus 2 (isolate Wuhan-Hu-1; NCBI NC_045512) were concatenated, indexed and used as a references for alignment.
STAR (version 2.7.9a) was used for indexing the combined reference genome and for mapping the sequenced reads to the combined genome reference sequences.
The aligned reads were indexed and sorted using samtools (version 1.10) and quantified with the featureCounts function of the subread (version 1.6.2) software.
Exploratory data analysis and differential expression analysis were performed using DESeq2 (version 1.34.0) using the counts data, after excluding the Gencode suffix from the Ensembl IDs of the mouse genes. False Discovery Rate was set to 0.05
Assembly: Mus musculus: GRCm39; Gencode version M27; Severe acute respiratory syndrome coronavirus 2: isolate Wuhan-Hu-1; NCBI NC_045512
Supplementary files format and content: tab-delimited text file includes raw counts as input matrix to DESeq2 (this file excludes the Gencode suffix)

organism: Mus musculus

source_name: Lung

extract_protocol:
RNA was extracted using Qiagen RNAeasy@ Plus micro kit. 100 ng was used for construction of sequencing libraries
RNA libraries were constructed following the ultra-low input protocol and paired-end sequencing (150 bp) was performed by Genewiz from Azenta Life Sciences (South Plainfield, NJ, USA)

value: Lung

value: Lung endothelial cells

value: 2 days post infection


title: Lung endothelial cells_Young_SARS-CoV-2 infected, biological replicate 3


title: 008T


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6300

description:
Yuka.aca.hic
Yuka_Loxafr3.0_HiC.hic
Yuka_Loxafr3.0_HiC_30.hic

organism: Mammuthus primigenius

source_name: trunk

value: trunk


title: Lung endothelial cells_Young_mock, biological replicate 3

value: Mock/PBS


title: 006T


title: 007N

value: Normal

value: Tumor tissue


title: pMF-HSC_C57Bl6/J_OSMI-1_rep4

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  SOAPnuke
Mapping of reads to the mouse genome was achieved using Bowtie2 (v2.3.5.1; parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200) using the GENCODE annotation GRCm39
Read counting was then performed using the RNA‑Seq by Expectation Maximization (RSEM, v1.3.1; parameters: -p 8 --forward-prob 0 --paired-end)
Normalization and differential gene expression analyses were performed using DESeq2 (v1.36.0). Genes with low expression (total read counts below 10) were removed and treatment and control samples from the same replicate were paired for differential expression analysis.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include Ensembl IDs and count values for each Sample
Supplementary files format and content: Matrix table include normalized abundance measurements (output from DESeq2 ; "OSMI1vsCtrl.complete.txt" file)

source_name: Primary myofibroblastic hepatic stellate cell

growth_protocol: Mice were housed in standard cages in a temperature-controlled room (22-24°C) with 12 hours (h) light-dark cycles and provided with water and standard diet ad libitum. Mice were allowed to acclimate for at least 1 week (wk) prior to any experiment. Quiescent primary mouse  HSCs were isolated from WT C57BL/6J mice (male, 15-18 wks old, Charles River) according to the protocol described in Bobowski-Gerard et al. (2022) and underwent spontaneous activation into myofibroblastic HSCs (MF-HSCs) upon regular in vitro cell culture for 7 days in Dulbecco’s Modified Eagle Medium (DMEM, GibcoTM) supplemented with 5% fetal bovine serum (FBS, Deutscher).

extract_protocol:
pMF-HSC total RNA was harvested using Nucleospin® RNA Plus XS kit (Macherey-Nagel).
RNA libraries for RNA-seq were prepared with DNBSEQ stranded mRNA library after oligo dT based enrichment

treatment_protocol: Primary mouse myofibroblastic HSCs (pMF-HSCs at 7 d of culture) were treated with vehicle (DMSO) or OSMI-1 at 50 µM for 24 h (4 biological replictates)


title: Lung endothelial cells_Young_SARS-CoV-2 infected, biological replicate 1


title: 007T

value: Normal renal tissue


title: bulkATACseq_CD34+_2DG_12h_rep1

description: bulk ATAC seq - Fast ATAC protocol

value: Umbilical cord blood

value: Healthy

value: CD34+ cells

value: 2DG 1mM


title: Lung endothelial cells_Young_mock, biological replicate 4


title: 006N


title: Lung endothelial cells_Young_mock, biological replicate 2


title: pMF-HSC_C57Bl6/J_OSMI-1_rep2

value: Primary myofibroblastic hepatic stellate cell


title: pMF-HSC_C57Bl6/J_Control_rep4

value: DSMO


title: 005T

value: Tumor


title: pMF-HSC_C57Bl6/J_OSMI-1_rep1


title: pMF-HSC_C57Bl6/J_Control_rep3

value: DMSO


title: 004T


title: Lung endothelial cells_aged_SARS-CoV-2 infected, biological replicate 4


title: pMF-HSC_C57Bl6/J_Control_rep2


title: Hi-C of Elephas maximus DNA Zoo Sample0030, part1

description:
HIC1381_ASM1433276v1_HiC.hic
HIC1381_ASM1433276v1_HiC_30.hic

value: blood:Ear vein


title: Lung endothelial cells_aged_SARS-CoV-2 infected, biological replicate 3

value: Lung


title: Lung endothelial cells_Young_SARS-CoV-2 infected, biological replicate 2

value: Lung endothelial cells


title: 008N


title: 004N


title: Lung endothelial cells_aged_SARS-CoV-2 infected, biological replicate 2

value: 2 days post infection


title: 003T


title: pMF-HSC_C57Bl6/J_Control_rep1


title: Lung endothelial cells_aged_SARS-CoV-2 infected, biological replicate 1


title: Lung endothelial cells_aged_mock, biological replicate 4


title: 003N


title: Lung endothelial cells_Young_mock, biological replicate 1


title: pMF-HSC_C57Bl6/J_OSMI-1_rep3


title: 001N


title: 001T


title: Lung endothelial cells_aged_mock, biological replicate 2


title: 002N


title: Lung endothelial cells_aged_mock, biological replicate 1


title: 005N


title: 3850 NC control f

status: Public on May 21 2024

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

description: Control

data_processing:
Trimmed sequence reads were mapped to mm10 using Banana Slug Analytics Platform (Slug Genomics, 203 UV Santa Cruz)
Cuffdiff were used for differential expression analysis (Slug Genomics, 203 UV Santa Cruz)
The Cuffdiff output was used to generate volcano plots (EnhancedVolcano) and ggplot (enrichplot)  using  R package 4.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Adipose tissue

extract_protocol:
Total RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA libraries for RNA-seq were prepared using TruSeq total RNA Library Prep Kit following manufacturer's protocols.

value: Adipose tissue

tag: group

value: normal chow


title: 1500 WD experimental f

description: Experiment

value: western diet to induce obesity


title: 3821 WD experimental f

description: Experiment


title: 1501 WD experimental f

description: Experiment


title: 1492 NC control f

description: Control


title: 002T


title: HiC, PS312, J2, rep2

first: Avrami

last: Aharonoff

address: 29 Washington Place

department: Biology

institute: New York University

data_processing:
hic files were generated using Juicer (version 1.5.7).
Assembly: PRJNA12644 (P. pacificus), PRJNA644888 (O. tipulae)
Supplementary files format and content: hic

organism: Pristionchus pacificus

growth_protocol: Pristionchus pacificus J2 larvae were isolated by filtering mixed stage worms through a 20 micron nylon mesh, and collecting the flow through. Oscheius tipulae early stage synchronized larvae were isolated by bleaching gravid adults, hatching embryos in M9, and growing synchronized L1 larvae on NGM plates supplemented agarose at 22˚C for 24 hours.

extract_protocol:
Larvae were resuspended in PBS with 1 mM PMSF. A mortar and pestle (BioSpec Products, catalog # 206) was placed on dry ice and filled with liquid nitrogen. Drops of larvae were pipetted into the mortar, and pulverized into a fine powder while submerged in liquid nitrogen. Powdered larvae were crosslinked as described in the Arima Hi-C+ High Coverage Kit (A101030), and Hi-C was performed as per the manufacturer’s instructions.
Library preparation was performed with the KAPA Hyper Prep Kit (KK8502) as per Arima’s instructions.

treatment_protocol: Larvae were treated with 2% formaldehyde for 30 minutes, washed with M9, collected by centrifugation, flash frozen with liquid nitrogen, and stored at -80˚C until extract preparation.

tag: source

value: whole worm

value: hermaphrodite

tag: strain

tag: developmental stage

tag: construction protocol

value: Arima HiC+ kit for high coverage


title: HiC, PS312, J2, rep1


title: 3846 NC control f

description: Control

tag: tissue


title: 1502 WD experimental f

description: Experiment


title: 3845 NC control f

description: Control


title: 1502 WD experimental l

description: Experiment


title: AKPS in PlexinB2 OE, ATAC, replicate 2

city: Basel

first: Costanza

last: Borrelli

address: Mattenstrasse 26

country: Switzerland

institute: ETH Zurich

description: 10x Genomics

data_processing:
BCL files were demultiplexed using Bcl2fastq v2.20.0.422 from Illumina, then single nucleus count matrices were generated using Cell Ranger Arc (10X Genomics) with GRCm38 v2020-A gene code
Assembly: GRCm38
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files.
Library strategy: Single Cell Multiome ATAC + Gene Expression

extract_protocol:
For each sample (2 sgNT and 2 sgPlxnb2 OE livers), three 50 μm liver sections were transferred into a pre-chilled gentleMACS C-tube (Miltenyi) and homogenized in the gentleMACS™ Octo Dissociator with 2 mL nuclei extraction buffer (Miltenyi). The nuclei suspension was filtered through a 70 µm SmartStrainer into a DNA-low binding 5 mL Tube (Eppendorf) and spun down at 150g for 3 minutes, at 4 °C. The pellet was resuspended in 5 mL 1% BSA in PBS and strained through a 30 µm SmartStrainer into a new tube. Upon centrifugation, the pellet was washed again in 5 mL 1% BSA in PBS. Nuclei were resuspended in 500 µL 1% BSA in PBS, counted and visually inspected.
16’000 nuclei per sample were profiled with the Chromium Single Cell Multiome ATAC + Gene Expression kit (10x) according to manufacturer’s instructions. Libraries were quality controlled and sequenced as described above.

value: liver

tag: genotype


title: AKPS in sgNT, RNA, replicate 2

description: 10x Genomics

tag: treatment


title: Lung endothelial cells_aged_mock, biological replicate 3

tag: cell type

value: Mock/PBS


title: AKPS in sgNT, ATAC, replicate 2

description: 10x Genomics


title: AKPS in PlexinB2 OE, RNA, replicate 2

description: 10x Genomics


title: 3821 WD experimental l

description: Experiment


title: 1500 WD experimental l

description: Experiment


title: 1492 NC control l

description: Control


title: 1501 WD experimental l

description: Experiment


title: 3850 NC control l

description: Control


title: AKPS in PlexinB2 OE, RNA, replicate 1

description: 10x Genomics


title: AKPS in sgNT, RNA, replicate 1

description: 10x Genomics


title: AKPS in PlexinB2 OE, ATAC, replicate 1

description: 10x Genomics


title: vehicle

description: 10x Genomics

data_processing:
BCL files were demultiplexed using Bcl2fastq v2.20.0.422 from Illumina, then single cell count matrices were generated using Cell Ranger (v5.0.0, 10X Genomics) with GRCm38 v2020-A gene code.
Assembly: GRCm38
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: colorectal cancer AKPS organoid

extract_protocol:
Cells were filtered, counted and loaded onto a GemCode Single-cell Instrument (10X Genomics).
Libraries were generated following the manufacturer’s instructions from Chromium Next GEM Single Cell 3’end Reagent Kits v1.1 protocol.

treatment_protocol: AKPS organoids were dissociated into single cells and incubated with 2μg/mL rmPlexin B2 or vehicle in culture medium for 2 hours at 37°C.

tag: cell line

value: colorectal cancer AKPS organoid

value: vehicle


title: 3845 NC control l

description: Control


title: rPlxnb2

description: 10x Genomics


title: 3846 NC control l

description: Control


title: RNAseq_mouse_gastruloids_120h_3

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

description: RNA-seq

data_processing:
Sequence reads were processed using the seq2science pipeline (v0.7.1, https://github.com/vanheeringen-lab/seq2science). In short, paired-end reads were trimmed with fastp (v0.20.1, default settings) and aligned with STAR (v2.7.6a, default settings) to the Mus musculus genome assembly GRCm38.p6. Aligned reads were filtered based on a minimum mapping quality of 255 and duplicate reads and reads in the ENCODE blacklisted regions were filtered out. Sample sequencing strandedness was inferred using RSeQC (v4.0.0) and number of reads per gene were measured with HTSeq count (v0.12.4). Deseq2 (v1.34.0) was used for downstream analysis.
Supplementary files format and content: counts

source_name: E14_triple reporter

growth_protocol: Mouse gastruloids were generated as previously described (Protoc. Exch. https://doi.org/10.1038/protex.2018.094, van den Brink et al., Nature 2020). Briefly, 300 single cells were FACS sorted with a BD FACSMelody™ cell sorter into U-bottomed 96 wells (Greiner Bio-one; 650185) containing 40μL NDiff227. After 48h, the aggregates were treated with 3μM CHIR99021 (Axon 1386) and medium was refreshed every day with pre-equilibrated NDiff227. For human somitoids, iPSCs were sorted with a BD FACSMelody™ cell sorter into U-bottomed 96 wells (Greiner Bio-one; 650970) (350cells/well) containing 50ul somitoid induction medium (NDiff227 supplemented with 10μM SB431542, 10μM CHIR99021, 2μM DMH1, and 20ng/ml bFGF with 10μM Y-27632 ROCK-inhibitor. After sorting, the plates were centrifuged for 2min at 150g. Twenty four hours after sorting, 150μl somitoid medium was added and medium was refreshed with NDiff227 at 48h and 72h. At 96h, medium was replaced with NDiff227 medium containing 10% matrigel.

extract_protocol:
RNA was extracted using Quick-RNA MicroPrep kit (Zymo Research) according to the manufacturer’s instruction with DNAseI treatment included.
For RNA-seq, libraries were generated from 40ng (human somitoids or 150ng (mouse gastruloids) RNA with the KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems). Fragmentation and priming were performed at 94°C for 6 min. NEXTflex DNA barcodes were used for adaptor ligation. Libraries were amplified with 11-14 PCR cycles followed by a two steps library amplification cleanup using a 0.8x bead-based cleanup and then an 1x bead cleanup.

value: E14_triple reporter

value: mouse gastruloids

value: BRA-GFP, SOX17-RFP, MT1-BFP

value: gastruloid differentiation


title: RNAseq_mouse_gastruloids_96h_3

description: RNA-seq


title: RNAseq_mouse_gastruloids_96h_1

description: RNA-seq


title: RNAseq_mouse_gastruloids_96h_2

description: RNA-seq


title: RNAseq_mouse_gastruloids_120h_2

description: RNA-seq


title: RNAseq_mouse_gastruloids_48h_3

description: RNA-seq


title: RNAseq_mouse_gastruloids_72h_2

description: RNA-seq


title: RNAseq_mouse_gastruloids_72h_3

description: RNA-seq


title: RNAseq_mouse_gastruloids_72h_1

description: RNA-seq


title: RNAseq_mouse_gastruloids_48h_2

description: RNA-seq


title: RNAseq_mouse_gastruloids_48h_1

description: RNA-seq


title: RNAseq_mouse_gastruloids_0h_3

description: RNA-seq

value: mESCs

value: ESLIF medium


title: RNAseq_mouse_gastruloids_0h_1

description: RNA-seq


title: RNAseq_mouse_gastruloids_0h_2

description: RNA-seq


title: AKPS in sgNT, ATAC, replicate 1

description: 10x Genomics


title: RNAseq_mouse_gastruloids_120h_1

description: RNA-seq


title: HL-60 IgG CM-444

city: Pamplona

first: Nahia

last: Gomez-Echarte

address: Avenida Pio XII, 55

country: Spain

institute: CIMA

data_processing:
The reads were aligned to the human genome hg38 (GRCh38.p13) for all the samples.
The Cut&Run samples were analyzed using the CUT&RUNtools pipeline with default settings and no filtering for 120bp fragments59. Peak calling was performed on deduplicated reads with macs2 version 2.2.6 using the respective IgG samples as control (for removing peaks), narrow peak calling and paired end settings, and a threshold of q=0.01.
Assembly: GRCh38.p13
Supplementary files format and content: Narrowpeak_clean files with chromosome coordinates of peaks for each sample.
Library strategy: CUT&RUN

growth_protocol: AML cell lines were maintained in RPMI-1640 medium containing L-Glutamine supplemented with 1% of penicillin-treptomycin, 2% HEPES Buffer and 20% of Fetal Bovine Serum.

extract_protocol:
CUT&RUN was performed with the kit CUTANA ChIC/CUT&RUN (Epicypher, 14-1048) following the manufacturer’s instructions. Briefly, 0.5 million of HL-60 cells were harvested and resuspended in 100ul wash buffer [20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, supplemented with Protease Inhibitor EDTA-Free tablet (Roche 11836170001)]. Activated Concanavalin A was incubated with cells at room temperature for 10min to let the cells bind to the beads. For each target protein factor, 0.5μg of BRD4 CUTANA CUT&RUN antibody (Cat No 13-2003, Epicypher), Acetyl-Histone H3 (Lys 9) (C5B11) rabbit monoclonal antibody diluted 1:50 (Cat No 9649T, Cell Signaling) or Acetyl-Histone H3 (Lys 27) (D5E4) XP rabbit monoclonal antibody diluted 1:100 (Cat No 8173T, Cell Signaling) was added to each sample and incubated in the antibody buffer (wash buffer +0.01% Digitonin and 2 mM EDTA) overnight at 4°C. Isotype control IgG was used as a negative control. The beads were then washed twice with digitonin buffer [wash buffer +0.01% Digitonin], and 2.5 μL pAG-MNase was added to each sample. After ten minutes of incubation at room temperature, excessive pAG-MNase was washed out by a two-time digitonin buffer wash. Then targeted chromatin was digested and released from cells by 2 h of incubation with the presence of 2 mM CaCl2 at 4°C. After incubation with stop buffer [340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/mL RNase A, 50 μg/mL Glycogen] for 10 min at 37ºC the supernatant containing CUT&RUN-enriched DNA was purified using the CUTANA DNA Purification kit (Epicypher).
Illumina sequencing libraries were prepared from 6 ng of purified CUT&RUN DNA using NEBNext UltraTM II DNA Library Prep Kit for Illumina, following the manufacturer’s instructions. For BRD4, some modifications were added following the protocol of Nan Liu (Harvard University; https://dx.doi.org/10.17504/protocols.io.wvgfe3w).

treatment_protocol: Panobinostat (HY-10224-CS-0267, MedChemExpress) and the synthesized molecule CM-444 resuspended in DMSO were added to cell plates resulting in a final concentration of 4.5 nM and 270 nM, respectively. For the negative control of the experiments, DMSO was diluted in culture medium in the same way as for the compounds in order to reach equal volumes of DMSO in all conditions.

value: Acute Myeloid Leukemia

value: WT

tag: cut&run antibody

value: IgG Negative Control (13-0042, Epicypher)


title: HL-60 H3K9ac C-

value: DMSO (control)

value: H3K9ac (9649T, Cell Signaling)


title: HL-60 H3K9ac Panobinostat

value: Panobinostat


title: HL-60 H3K27ac C-

value: H3K27ac (8173T, Cell Signaling)


title: HL-60 H3K27ac CM-444


title: HL-60 H3K27ac Panobinostat


title: HL-60 BRD4 C-

value: BRD4 (13-2003, Epicypher)


title: HL-60 IgG C-


title: HL-60 BRD4 Panobinostat


title: HL-60 IgG Panobinostat


title: HL-60 H3K9ac CM-444


title: n3 lean control

description: Control

value: Adipose tissue

value: lean


title: n5 lean control

description: Control


title: n7 obese experimental

description: Experiment

value: obese


title: n6 obese experimental

description: Experiment


title: n8 obese experimental

description: Experiment


title: n1 obese experimental

description: Experiment


title: RNAseq_human_somitoids_ZEB2_HomKO_3

description: RNA-seq

source_name: MML-6838-Cl2 iPSCs

value: MML-6838-Cl2 iPSCs

value: human iPSCs

value: homozygous ZEB2 knockout

value: somitoid differentiation


title: n4 obese experimenrtal

description: Experiment


title: RNAseq_human_somitoids_ZEB2_HomKO_1

description: RNA-seq


title: RNAseq_human_somitoids_ZEB2_HomKO_2

description: RNA-seq


title: RNAseq_human_somitoids_ZEB2_HetKO_3

description: RNA-seq

value: heterozygous ZEB2 knockout


title: RNAseq_human_somitoids_ZEB2_HetKO_2

description: RNA-seq


title: RNAseq_human_somitoids_ZEB2_HetKO_1

description: RNA-seq


title: RNAseq_human_somitoids_WT_1

description: RNA-seq

value: wildtype


title: RNAseq_human_somitoids_WT_2

description: RNA-seq


title: RNAseq_human_somitoids_WT_3

description: RNA-seq


title: HL-60 BRD4 CM-444

value: Acute Myeloid Leukemia


title: HiC, CEW1, early stage synchronized larvae, rep 2

organism: Oscheius tipulae

value: whole worm

value: hermaphrodite

value: early stage synchronized larvae

value: Arima HiC+ kit for high coverage


title: n9 lean control

description: Control


title: HiC, CEW1, early stage synchronized larvae, rep 1


title: E. coli strain AP, engineered strain, rep 2

city: Tianjin

first: Lixia

last: Fang

address: 135 Yaguan Road, Jinnan District

institute: Tianjin University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6) by removing reads containing sequencing adapter, reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20% and reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com). HISAT2 (v2.1.0) was applied to align the clean reads to the reference genome. Bowtie2 (v2.3.4.3) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Expression level of gene was calculated by RSEM (v1.3.1). Essentially, differential expression analysis was performed using the DESeq2 (v1.4.5) with Q value <= 0.05. KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value <= 0.05).
Assembly: GCF_000005845.2_ASM584v2
Supplementary files format and content: Excel file-gene expression (fpkm, read, log2 fold change, and q-value)

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacteria

growth_protocol: The A (CF) and AP (pcnBi) strains were cultivated in modified M9 medium at 30℃ and inducted by IPTG when OD600 reached about 1.

extract_protocol:
Total RNA was extracted using the RiboPure™ Bacteria Kit (Invitrogen, USA) following the manufacturer’s recommendations. RNA quality was checked using the DNF-471 Standard Sensitivity RNA Analysis Kit (Agilent, USA) and running on Fragment Analyzer (Agilent, USA). RNA sample was treated with DNase-I to remove DNA and was subjected to TIANSeq rRNA Depletion Kit (G- Bacteria) (TIANGEN, China) to remove rRNA.
Sequencing libraries were constructed using the Optimal Dual-mode mRNA Library Prep Kit (BGI, China) following the manufacturer’s instructions. Circularization was performed using the MGIEasy Circularization Kit (MGI, China) and the product was quantitated using the Qubit® ssDNA Assay Kit (Invitrogen, USA). The libraries were then prepared using the MGISEQ-2000RS High-throughput Sequencing Set (FCL PE100) (MGI, China) and sequenced via the DNBSEQ-G400 platform (BGI, China) according to the manufacturer’s instructions.

treatment_protocol: Cells were harvested after 12 h of IPTG induction by quick centrifugation at 4℃, 12,000 rpm for 1 min, and immediately frozen in liquid nitrogen.

value: bacteria


title: E. coli strain A, control strain, rep 2


title: E. coli strain A, control strain, rep 1


title: E. coli strain A, control strain, rep 3


title: E. coli strain AP, engineered strain, rep 1


title: E. coli strain AP, engineered strain, rep 3


title: AAV Liver, HBV Infected + Vehicle, Day 70 rep 2

city: Foster City

first: Cameron

last: Soulette

address: 333 Lakeside Dr

institute: Gilead Sciences

description:
Mouse
39_Day_70
aav-hbv_rawcounts.csv

data_processing:
Gene counts files were generated.
Assembly: Hg38 & mm10
Supplementary files format and content: csv, gene counts

source_name: Liver

extract_protocol:
polyA
Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103)
HiSeq-Sequencing-2x50bp-PE sequencing on an Illumina sequencing platform
Briefly, Total RNA samples are concentration normalized, and polyadenylated RNA is purified using oligo-dT attached to magnetic beads. Purified mRNA is fragmented using heat in the presence of divalent cations. Fragmented RNA is converted into double-stranded cDNA, with dUTP utilized in place of dTTP in the second strand master mix. A single ‘A’ base is added to the cDNA and forked adaptors that include index, or barcode, sequences are attached via ligation. The resulting molecules are amplified via polymerase chain reaction (PCR). During PCR the polymerase stalls when a dUTP base is encountered in the template. Since only the second strand includes the dUTP base, this renders the first strand the only viable template, thereby preserving the strand information. Final libraries are quantified, normalized and pooled. Pooled libraries are bound to the surface of a flow cell and each bound template molecule is clonally amplified up to 1000-fold to create in- dividual clusters. Four fluorescently labeled nucleotides are then flowed over the surface of the flow cell and incorporated into each nucleic acid chain. Each nucleotide label acts as a terminator for polymerization, thereby en- suring that a single base is added to each nascent chain during each cycle. Fluorescence is measured for each cluster during each cycle to identify the base that was added to each cluster. The dye is then enzymatically removed to allow incorporation of the next nucleotide during the next cycle.

value: Liver

value: AAV Liver

value: HBV Infected + Vehicle, Day 70


title: PBMCs_OPN5_2

type: RNA

city: Omaha

first: Dalia

last: El-Gamal

state: NE

address: 986805 NE Med Center BCC 4.12.396

department: Eppley Institute

institute: University of Nebraska Medical Center

hyb_protocol: Performed according to NanoString protocol for the PanCancer IO 360™ Panel at the UNMC Genomics Core Facility

scan_protocol: Performed according to NanoString protocol on an nCounter Pro Analysis System at the UNMC Genomics Core Facility

data_processing: Data was acquired by the University of Nebraska Medical Center (UNMC) Genomics Core using an nCounter Pro Analysis System. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC steps. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. The nCounter® Advanced Analysis protocol was followed to divide counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library. Abundance of various cell populations is calculated using the Nanostring Cell Type Profiling Module. Fold changes and p-values are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Several database sources were referenced for enrichment analysis, including Integrated Pathway Anlaysis (IPA), MSigDB, and EnrichR.

label: NanoString

source_name: PBMCs from Eμ-TCL1 adoptive transfer mice, treated for 4 weeks with OPN-51107

growth_protocol: Wild-type C57BL/6J mice (8 weeks old) were engrafted with 1e7 spleen-derived lymphocytes from a moribund Eμ-TCL1 mouse. Once mice displayed evident disease in the peripheral blood (2 weeks post-engraftment), they were randomize to receive treatment with OPN-51107 or vehicle control. Mice were sacrificied for tissue sequencing after 3 weeks of treatment.

extract_protocol: Murine splenocytes or peripheral blood mononuclear cells (PBMCs) were homogenized into a single cell suspension, then 1e7 cells were pelleted and snap frozen for each sample. Total RNA was isolated using RNeasy Mini Kit (Qiagen; Hilden, Germany) following manufacturer instructions. RNA was cleaned up via DNAse and ethanol treatment. RNA quantity and quality was assesed using a Qubit fluorometer (Thermo Fisher Scientific) and fragment analysis was performed with Bioanalyzer (Agilent) prior sequencing.

treatment_protocol: Mice were treated via oral gavage with 20 mg/kg OPN-51107 dissolved in [10% N-methyl-2-pyrrolidone plus diluent (40% PEG400, 5% TPGS, 5% Poloxamer 407, and 50% water)] or vehicle equivalent, daily for 3 weeks.

value: Peripheral blood mononuclear cells


title: PBMCs_OPN5_1

label_protocol: Performed according to NanoString protocol for the PanCancer IO 360™ Panel at the UNMC Genomics Core Facility


title: AAV Liver, HBV Infected + Vehicle, Day 70 rep 3

description:
Mouse
38_Day_70
aav-hbv_rawcounts.csv


title: Spleen_OPN5_1

source_name: Spleen from Eμ-TCL1 adoptive transfer mice, treated for 4 weeks with OPN-51107

value: Spleen


title: Spleen_OPN5_2


title: PBMCs_VEH_3

source_name: PBMCs from Eμ-TCL1 adoptive transfer mice, treated for 4 weeks with vehicle control

value: Vehicle


title: PBMCs_OPN5_3


title: Spleen_OPN5_3


title: AAV Liver, HBV Infected + Vehicle, Day 70 rep 1

description:
Mouse
40_Day_70
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 70 rep 4

description:
Mouse
72_Day_70
aav-hbv_rawcounts.csv

value: HBV Infected + Treatment, Day 70


title: Spleen_VEH_1

source_name: Spleen from Eμ-TCL1 adoptive transfer mice, treated for 4 weeks with vehicle control


title: Spleen_VEH_2


title: AAV Liver, HBV Infected + Treatment, Day 70 rep 3

description:
Mouse
73_Day_70
aav-hbv_rawcounts.csv


title: PBMCs_VEH_2


title: AAV Liver, HBV Infected + Treatment, Day 70 rep 2

description:
Mouse
74_Day_70
aav-hbv_rawcounts.csv


title: Spleen_VEH_3


title: AAV Liver, HBV Infected + Vehicle, Day 70 rep 4

description:
Mouse
37_Day_70
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 70 rep 1

description:
Mouse
75_Day_70
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 70 rep 5

description:
Mouse
36_Day_70
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 56 rep 5

description:
Mouse
31_Day_56
aav-hbv_rawcounts.csv

value: HBV Infected + Vehicle, Day 56


title: AAV Liver, HBV Infected + Treatment, Day 70 rep 5

description:
Mouse
71_Day_70
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 56 rep 4

description:
Mouse
32_Day_56
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 56 rep 3

description:
Mouse
33_Day_56
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 56 rep 2

description:
Mouse
34_Day_56
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 56 rep 5

description:
Mouse
66_Day_56
aav-hbv_rawcounts.csv

value: HBV Infected + Treatment, Day 56


title: AAV Liver, HBV Infected + Treatment, Day 56 rep 3

description:
Mouse
68_Day_56
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 56 rep 1

description:
Mouse
35_Day_56
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 56 rep 2

description:
Mouse
69_Day_56
aav-hbv_rawcounts.csv


title: PBMCs_VEH_1


title: AAV Liver, HBV Infected + Vehicle, Day 38 rep 2

description:
Mouse
29_Day_38
aav-hbv_rawcounts.csv

value: HBV Infected + Vehicle, Day 38


title: AAV Liver, HBV Infected + Vehicle, Day 38 rep 1

description:
Mouse
30_Day_38
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 56 rep 1

description:
Mouse
70_Day_56
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 38 rep 3

description:
Mouse
63_Day_38
aav-hbv_rawcounts.csv

value: HBV Infected + Treatment, Day 38


title: AAV Liver, HBV Infected + Vehicle, Day 38 rep 4

description:
Mouse
27_Day_38
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 38 rep 3

description:
Mouse
28_Day_38
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 38 rep 1

description:
Mouse
65_Day_38
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 38 rep 5

description:
Mouse
26_Day_38
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 24 rep 2

description:
Mouse
24_Day_24
aav-hbv_rawcounts.csv

value: HBV Infected + Vehicle, Day 24


title: AAV Liver, HBV Infected + Vehicle, Day 24 rep 3

description:
Mouse
23_Day_24
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 38 rep 2

description:
Mouse
64_Day_38
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 24 rep 5

description:
Mouse
21_Day_24
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 24 rep 4

description:
Mouse
22_Day_24
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 24 rep 1

description:
Mouse
25_Day_24
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 38 rep 4

description:
Mouse
62_Day_38
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 24 rep 5

description:
Mouse
56_Day_24
aav-hbv_rawcounts.csv

value: HBV Infected + Treatment, Day 24


title: AAV Liver, HBV Infected + Treatment, Day 24 rep 2

description:
Mouse
59_Day_24
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 24 rep 4

description:
Mouse
57_Day_24
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 24 rep 3

description:
Mouse
58_Day_24
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 24 rep 1

description:
Mouse
60_Day_24
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 38 rep 5

description:
Mouse
61_Day_38
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 56 rep 4

description:
Mouse
67_Day_56
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 10 rep 5

description:
Mouse
16_Day_10
aav-hbv_rawcounts.csv

value: HBV Infected + Vehicle, Day 10


title: AAV Liver, HBV Infected + Vehicle, Day 10 rep 4

description:
Mouse
17_Day_10
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 10 rep 2

description:
Mouse
19_Day_10
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 10 rep 1

description:
Mouse
20_Day_10
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 10 rep 5

description:
Mouse
51_Day_10
aav-hbv_rawcounts.csv

value: HBV Infected + Treatment, Day 10


title: AAV Liver, HBV Infected + Treatment, Day 10 rep 2

description:
Mouse
54_Day_10
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 10 rep 3

description:
Mouse
53_Day_10
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 7 rep 5

description:
Mouse
15_Day_7
aav-hbv_rawcounts.csv

value: HBV Infected + Vehicle, Day 7


title: AAV Liver, HBV Infected + Vehicle, Day 7 rep 1

description:
Mouse
11_Day_7
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 7 rep 3

description:
Mouse
13_Day_7
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 10 rep 1

description:
Mouse
55_Day_10
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 7 rep 4

description:
Mouse
14_Day_7
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 7 rep 4

description:
Mouse
49_Day_7
aav-hbv_rawcounts.csv

value: HBV Infected + Treatment, Day 7


title: AAV Liver, HBV Infected + Vehicle, Day 3 rep 5

description:
Mouse
10_Day_3
aav-hbv_rawcounts.csv

value: Liver

value: HBV Infected + Vehicle, Day 3


title: AAV Liver, HBV Infected + Treatment, Day 7 rep 5

description:
Mouse
50_Day_7
aav-hbv_rawcounts.csv

value: AAV Liver


title: AAV Liver, HBV Infected + Vehicle, Day 3 rep 4

description:
Mouse
9_Day_3
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 3 rep 2

description:
Mouse
7_Day_3
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 3 rep 3

description:
Mouse
8_Day_3
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 7 rep 1

description:
Mouse
46_Day_7
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 7 rep 2

description:
Mouse
47_Day_7
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 3 rep 1

description:
Mouse
6_Day_3
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 7 rep 3

description:
Mouse
48_Day_7
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 3 rep 5

description:
Mouse
45_Day_3
aav-hbv_rawcounts.csv

value: HBV Infected + Treatment, Day 3


title: AAV Liver, HBV Infected + Treatment, Day 3 rep 3

description:
Mouse
43_Day_3
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 3 rep 2

description:
Mouse
42_Day_3
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 3 rep 4

description:
Mouse
44_Day_3
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Vehicle, Day 10 rep 3

description:
Mouse
18_Day_10
aav-hbv_rawcounts.csv


title: AAV Liver, HBV Infected + Treatment, Day 3 rep 1

description:
Mouse
41_Day_3
aav-hbv_rawcounts.csv


title: neutrophils, OV68, HKAF+CsA

city: Brno

first: Ioanna

last: Papatheodorou

address: Studentska

department: Center for Translational Medicine

country: Czech Republic

institute: International Clinical Research Center (ICRC), St.Anne’s Hospital

data_processing:
Sequences were trimmed for adaptors/low quality sequences using Trim galore with default parameters.
Trimmed sequences were mapped to GRCh38-p10 (human genome) with HISAT2 using the default parameteres.
Read counts were determined with Htseq -count.
Raw gene counts were normalized following VST transformation by use of the package DESeq2 in the R v4.3.3. environment.
Differentially expressed genes were determined with DESeq2 in the R v4.3.3. enviroment.
Genes were considered significantly differentially expressed when they demonstrated a log fold change of |LFC| >= 0.6 and p-value =< 0.05
Assembly: GRCh38-p10
Supplementary files format and content: The txt delimited file named Raw_counts_neutrophils_dataset.txt contains all the raw HTseq derived counts.
Supplementary files format and content: The txt delimited file named Normalized_counts_neutrophils_dataset.txt contains all the normalized counts following VST transformation.

growth_protocol: Freshly isolated neutrophils were maintained in X-VIVO 15 media (Lonza) in concentration 2 × 10^6 cells/ml.

extract_protocol:
Total RNA was extracted using the Arcturus Pico pure kit (Life Technologies). Total RNA was then used for the construction of the libraries.
Illumina sequencing libraries were prepared using the Lexogen Quantseq FWD kit following the manufacturer’s instructions.

treatment_protocol: Neutrophils were pre-treated with either 2 𝜇g/ml CsA or 0.4 𝜇g/ml FK506 for 1 hour. The cells were then exposed to heat-killed fungal pathogens Candida ablicans (HKCA) or Aspergilus fumigatus (HKAF) for 2 hours.

value: blood

value: primary neutrophils

value: WT

value: Aspergillus fumigatus + Cyclosporine A


title: neutrophils, OV68, HKCA+CsA

value: Candida albicans + Cyclosporine A


title: AAV Liver, HBV Infected + Treatment, Day 10 rep 4

description:
Mouse
52_Day_10
aav-hbv_rawcounts.csv


title: neutrophils, OV68, HKCA

value: Candida albicans


title: neutrophils, OV68, NT+CsA

value: Cyclosporine A


title: neutrophils, OV68, NT

value: Non treated


title: AAV Liver, HBV Infected + Vehicle, Day 7 rep 2

description:
Mouse
12_Day_7
aav-hbv_rawcounts.csv


title: neutrophils, OV67, HKCA+CsA


title: neutrophils, OV67, HKCA


title: neutrophils, OV67, HKAF

value: Aspergillus fumigatus


title: neutrophils, OV67, NT


title: neutrophils, OV67, HKAF+CsA


title: neutrophils, OV66, HKAF


title: neutrophils, OV62, NT+CsA


title: neutrophils, OV66, HKAF+CsA


title: neutrophils, OV66, HKCA


title: neutrophils, OV66, NT


title: neutrophils, OV62, HKAF


title: neutrophils, OV66, HKCA+CsA


title: neutrophils, OV62, HKCA+CsA


title: neutrophils, OV62, NT


title: neutrophils, OV62, HKAF+CsA


title: neutrophils, OV68, HKAF


title: neutrophils, OV62, HKCA


title: RNA-seq: Infected WT LV-rec 19

city: Natal

first: Selma

middle: MB

last: Jeronimo

state: Rio Grande do Norte

address: 655 Av Passeio dos Girassois, Capim Macio

department: Tropical Medicine Institute (IMT-RN)

country: Brazil

institute: Federal University of Rio Grande do Norte (UFRN)

description:
17.INF.lane1
17.INF.lane2
17.INF.lane3

data_processing:
Illumina HiSeq 2000 (75 bp, paired-end), each sample with 3 experimental replicates (with the exception of participant 6, who has only an experimental duplicate in the infected sample.)
Aligmntent HISAT2 2.2.0 in default parameters
Files were compressed into BAM using Samtools 1.15
The counts assigned were accessed by FeatureCounts
Differential expression analysis: DESeq2 3.14 (Bioconductor)
Assembly: GRCh38
Supplementary files format and content: Gene counts matrix from FeatureCounts of all samples together

source_name: monocytes-derived macrophages

growth_protocol: PBMC were maintained in RPMI 1640 supplemented with 1.5μM L-glutamine, 1mM Hepes, 10% heat-inactivated AB human serum and 5ng/mL of M-CSF (Gibco, USA) to obtain monocytes-derived macrophages.

extract_protocol:
RNA extraction was performed using the standard Trizol protocol, followed by purification in the Qiagen column. The quality of the RNA was checked using the NanoDrop spectrometer (NanoDrop Technologies), Agilent Bioanalyzer (RNA Nano Chip, Agilent) and also by Qubit 2.0 / 3.0 fluorometer.
20 ul of total RNA (75-350 ng/ul) were submitted to the sequencing facility and default protocol was carried on.

treatment_protocol: Infection with L. infantum (Strain isolated from a patient diagnosed with VL in Natal, RN, Brazil) proceeded in the monocyte-derived macrophages. Leishmania stationary promastigotes at a 5 parasites/cell ratio were incubated for 2 hours. After the incubation, free parasites were washed with warm RPMI 1640. Infected MØ for sequencing were aliquoted at 72 hours after infection.

value: monocytes-derived macrophages

value: male

value: Infected (Leishmania infantum)


title: RNA-seq: Non-Infected WT LV-rec 19

description:
17.NO.lane1
17.NO.lane2
17.NO.lane3

value: Non-infected


title: RNA-seq: Non-Infected WT LV-rec 16

description:
14.NO.lane1
14.NO.lane2
14.NO.lane3

value: female


title: neutrophils, OV67, NT+CsA

source_name: blood


title: RNA-seq: Non-Infected WT 15

description:
10.NO.lane1
10.NO.lane2
10.NO.lane3


title: RNA-seq: Infected WT LV-rec 18

description:
16.INF.lane1
16.INF.lane2
16.INF.lane3


title: Sample 15_04H096

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Fastqs were processed by CellRanger version 5 with GEX fastq (samples 1-17) or GEX and ADT fastqs (pool of samples 18).
Sample 17 was multiplexed with other samples not part of the analysis, the FastQs pertaining to this sample were subsetted from the original FastQs
Filtered counts output from CellRanger are provided for samples 1-16 and 18 whereas raw counts are provided for sample 17.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: cell barcodes
Supplementary files format and content: features.tsv.gz: genes detected
Supplementary files format and content: matrix.mtx.gz: cell by gene expression matrix

source_name: Bone marrow

extract_protocol: 10X Chromium Single Cell 3'

value: Bone marrow

value: Primary acute myeloid leukemia cells

value: mono 7

value: Male


title: RNA-seq: Infected WT 15

description:
10.INF.lane1
10.INF.lane2
10.INF.lane3


title: RNA-seq: Non-Infected WT LV-rec 17

description:
15.NO.lane1
15.NO.lane2
15.NO.lane3


title: RNA-seq: Infected WT LV-rec 16

description:
14.INF.lane1
14.INF.lane2
14.INF.lane3


title: RNA-seq: Non-Infected WT 14

description:
9.NO.lane1
9.NO.lane2
9.NO.lane3


title: RNA-seq: Non-Infected WT 13

description:
5.NO.lane1
5.NO.lane2
5.NO.lane3


title: RNA-seq: Infected WT 13

description:
5.INF.lane1
5.INF.lane2
5.INF.lane3


title: neutrophils, OV66, NT+CsA

value: blood

value: primary neutrophils


title: RNA-seq: Non-Infected WT 12

description:
4.NO.lane1
4.NO.lane2
4.NO.lane3

value: WT


title: RNA-seq: Infected WT 14

description:
9.INF.lane1
9.INF.lane2
9.INF.lane3


title: Sample 16_05H193


title: RNA-seq: Infected WT 12

description:
4.INF.lane1
4.INF.lane2
4.INF.lane3


title: RNA-seq: Infected BSCL2het 11

description:
2.INF.lane1
2.INF.lane2
2.INF.lane3

value: BSCL2 heterozygous


title: RNA-seq: Infected BSCL2het 9

description:
13.INF.lane1
13.INF.lane2
13.INF.lane3


title: RNA-seq: Non-Infected BSCL2het 8

description:
12.NO.lane1
12.NO.lane2
12.NO.lane3


title: RNA-seq: Infected BSCL2mut 6

description:
3.INF.lane1
3.INF.lane2

value: BSCL2 mutated


title: RNA-seq: Non-Infected BSCL2het 7

description:
11.NO.lane1
11.NO.lane2
11.NO.lane3


title: RNA-seq: Non-Infected WT LV-rec 18

description:
16.NO.lane1
16.NO.lane2
16.NO.lane3


title: RNA-seq: Non-Infected BSCL2mut 6

description:
3.NO.lane1
3.NO.lane2
3.NO.lane3


title: RNA-seq: Non-Infected BSCL2mut 5

description:
19.NO.lane1
19.NO.lane2
19.NO.lane3


title: RNA-seq: Infected BSCL2mut 5

description:
19.INF.lane1
19.INF.lane2
19.INF.lane3


title: RNA-seq: Infected BSCL2mut 4

description:
18.INF.lane1
18.INF.lane2
18.INF.lane3


title: RNA-seq: Non-Infected BSCL2mut 4

description:
18.NO.lane1
18.NO.lane2
18.NO.lane3


title: RNA-seq: Non-Infected AGPAT2mut 3

description:
8.NO.lane1
8.NO.lane2
8.NO.lane3

value: AGPAT2 mutated


title: RNA-seq: Non-Infected AGPAT2mut 2

description:
7.NO.lane1
7.NO.lane2
7.NO.lane3


title: RNA-seq: Infected AGPAT2mut 3

description:
8.INF.lane1
8.INF.lane2
8.INF.lane3


title: RNA-seq: Non-Infected AGPAT2mut 1

description:
6.NO.lane1
6.NO.lane2
6.NO.lane3


title: RNA-seq: Infected AGPAT2mut 1

description:
6.INF.lane1
6.INF.lane2
6.INF.lane3


title: RNA-seq: Infected AGPAT2mut 2

description:
7.INF.lane1
7.INF.lane2
7.INF.lane3


title: 4T1 spheroids, transduced with shTlr7, replicate 1

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

country: Germany

institute: Charité University Medicine

data_processing:
Assembly: GRCm38
Sequencing reads were mapped to the GRCm38 genome using STAR aligner (v2.7.5) at default settings.
Reads mapping to genes were counted using STAR (v2.7.5).
Differentially expressed genes were determined using DESeq2 (v1.32.0).
Gene set enrichment analysis was performed using the gseKEGG function of the clusterProfiler package (v4.0.0). As input, genes were ranked according to their log fold changes shrunken with the ashr method of the DESeq2 package (v1.32.0)
Supplementary files format and content: tab-delimited file contains raw read counts for every sample.

source_name: spheroid generated from cell line

growth_protocol: Spheroids were formed with the hanging drop method and maintained in DMEM with 10% FBS at 37ºC and 5% CO2.

extract_protocol:
RNA was extracted using the Total RNA kit (Norgen) following manufacturer's instructions.
500ng of total RNA was used as input for the TruSeq RNA Library Prep Kit (Illumina) following manufacturer's instructions.

treatment_protocol: 4T1 cells were transduced with a lentivirus encoding either a control (scrambled) shRNA or Tlr7-targeting shRNA.

value: spheroid generated from cell line

value: breast cancer cells

value: expression of shTlr7


title: 4T1 spheroids, transduced with shTlr7, replicate 2


title: 4T1 spheroids, transduced with shTlr7, replicate 4


title: 4T1 spheroids, transduced with shCtrl, replicate 4

value: shCtrl

value: expressinon of scrambled shRNA


title: 4T1 spheroids, transduced with shTlr7, replicate 3


title: 4T1 spheroids, transduced with shCtrl, replicate 2


title: RNA-seq: Infected BSCL2het 7

description:
11.INF.lane1
11.INF.lane2
11.INF.lane3

value: monocytes-derived macrophages

value: male

value: Infected (Leishmania infantum)


title: RNA-seq: Non-Infected BSCL2het 9

description:
13.NO.lane1
13.NO.lane2
13.NO.lane3

value: Non-infected


title: 4T1 spheroids, transduced with shCtrl, replicate 1